4AC5 | pdb_00004ac5

Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb4AC5/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Blastochloris viridis
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2011-12-14 Released: 2012-02-15 
• Deposition Author(s): Johansson, L.C., Arnlund, D., White, T.A., Katona, G., DePonte, D.P., Weierstall, U., Doak, R.B., Shoeman, R.L., Lomb, L., Malmerberg, E., Davidsson, J., Nass, K., Liang, M., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M.J., Bostedt, C., Bozek, J.D., Caleman, C., Coffee, R., Coppola, N., Ekeberg, T., Epp, S.W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C.Y., Hartmann, R., Hartmann, A., Hauser, G., Hirsemann, H., Holl, P., Hunter, M.S., Kassemeyer, S., Kimmel, N., Kirian, R.A., Maia, F.R.N.C., Marchesini, S., Martin, A.V., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M.M., Sierra, R., Soltau, H., Starodub, D., Stellato, F., Stern, S., Struder, L., Timneanu, N., Ullrich, J., Wahlgren, W.Y., Wang, X., Weidenspointner, G., Wunderer, C., Fromme, P., Chapman, H.N., Spence, J.C.H., Neutze, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 8.20 Å
• R-Value Free: 
  0.384 (Depositor), 0.376 (DCC) 
• R-Value Work: 
  0.351 (Depositor), 0.343 (DCC) 
• R-Value Observed: 
  0.352 (Depositor) 

Starting Model: experimental

Literature

Lipidic Phase Membrane Protein Serial Femtosecond Crystallography.

Johansson, L.C., Arnlund, D., White, T.A., Katona, G., Deponte, D.P., Weierstall, U., Doak, R.B., Shoeman, R.L., Lomb, L., Malmerberg, E., Davidsson, J., Nass, K., Liang, M., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M.J., Bostedt, C., Bozek, J.D., Caleman, C., Coffee, R., Coppola, N., Ekeberg, T., Epp, S.W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C.Y., Hartmann, R., Hartmann, A., Hauser, G., Hirsemann, H., Holl, P., Hunter, M.S., Kassemeyer, S., Kimmel, N., Kirian, R.A., Maia, F.R.N.C., Marchesini, S., Martin, A.V., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M.M., Sierra, R., Soltau, H., Starodub, D., Stellato, F., Stern, S., Struder, L., Timneanu, N., Ullrich, J., Wahlgren, W.Y., Wang, X., Weidenspointner, G., Wunderer, C., Fromme, P., Chapman, H.N., Spence, J.C.H., Neutze, R.

(2012) Nat Methods 9: 263

• PubMed: 22286383 
• DOI: https://doi.org/10.1038/nmeth.1867
• Primary Citation Related Structures: 
  4AC5


• PubMed Abstract: 
  

  X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.82 kDa 
• Atom Count: 9,835 
• Modeled Residue Count: 1,171 
• Deposited Residue Count: 1,192 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT	A [auth C]	336	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173  Go to UniProtKB:  P07173

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN H CHAIN	B [auth H]	258	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008  Go to UniProtKB:  P06008

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN L CHAIN	C [auth L]	274	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009  Go to UniProtKB:  P06009

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN M CHAIN	D [auth M]	324	Blastochloris viridis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010  Go to UniProtKB:  P06010

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCB	I [auth L], J [auth L], L [auth M], M	BACTERIOCHLOROPHYLL B C55 H72 Mg N4 O6 QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB	K [auth L], N [auth M]	BACTERIOPHEOPHYTIN B C55 H74 N4 O6 SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7	P [auth M]	MENAQUINONE-7 C46 H64 O2 RAKQPZMEYJZGPI-LJWNYQGCSA-N
HEM	E [auth C], F [auth C], G [auth C], H [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NS5	Q [auth M]	15-cis-1,2-dihydroneurosporene C40 H60 NHKJSVKSSGKUCH-DBWJSHEJSA-N
FE2	O [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	B [auth H]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 8.20 Å
• R-Value Free:  0.384 (Depositor), 0.376 (DCC) 
• R-Value Work:  0.351 (Depositor), 0.343 (DCC) 
• R-Value Observed: 0.352 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.5	α = 90
b = 84.6	β = 90
c = 375.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
MONTE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Johansson, L.C., Arnlund, D., White, T.A., Katona, G., DePonte, D.P., Weierstall, U., Doak, R.B., Shoeman, R.L., Lomb, L., Malmerberg, E., Davidsson, J., Nass, K., Liang, M., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M.J., Bostedt, C., Bozek, J.D., Caleman, C., Coffee, R., Coppola, N., Ekeberg, T., Epp, S.W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C.Y., Hartmann, R., Hartmann, A., Hauser, G., Hirsemann, H., Holl, P., Hunter, M.S., Kassemeyer, S., Kimmel, N., Kirian, R.A., Maia, F.R.N.C., Marchesini, S., Martin, A.V., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M.M., Sierra, R., Soltau, H., Starodub, D., Stellato, F., Stern, S., Struder, L., Timneanu, N., Ullrich, J., Wahlgren, W.Y., Wang, X., Weidenspointner, G., Wunderer, C., Fromme, P., Chapman, H.N., Spence, J.C.H., Neutze, R.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-03-14
  Changes: Other
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2018-02-14
  Changes: Data collection
• Version 1.4: 2018-11-14
  Changes: Data collection
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-11-06
  Changes: Structure summary